They check your job reference letters against the main statement and duties listed on the NOC that you applied for and specify in the forms. The form asks for both NOC code and "occupation", and some NOCs cover more than one occupation, so my NOC 2174 covers Computer Programmers AND Interactive Media Developers and I wrote "Computer Programmer". If your job title was "Senior Commercial Conveyancer" you might write your occupation as "lawyer" for example.
The NOC then lists "example" job titles for those occupations.
In the occupation box it is best to write your occupation rather than job title, but if your job title is similar to those listed on the NOC page then writing it shouldn't have any adverse effect at all. Plenty of people will have put their "Job Title" in the "Occupation" box and many will get through fine. Obviously if you put your occupation as "Metallurgist" and a NOC of 2174 (Computer Programmer) then you could expect some issues